Monday, January 23, 2012

New metadata browsing and management

The metadata vocabulary is a very useful component of our Browser. It organizes hundreds or thousands of data tracks in a meaningful way, underlies the metadata color map, and allows creation of custom entries. Before this date, the metadata system hasn't been well designed -- repetitive components and duplicative code, cluttered user interface and rigid usability.

Now it has got a complete redesign! Highlights are following:

  1. New interface to a centralized metadata user interface, allowing you to browse and manage metadata at one place. Code duplication and forking has thus been eliminated.
  2. Editing metadata for custom bigwig tracks.

1. New metadata management system

At control panel of the Browser, click tab "Metadata" to find the metadata browser panel:


Shown are root level terms of metadata vocabulary of human database. Click on a term to navigate through the vocabulary:


Check a checkbox to have the term displayed as one column in metadata color map:


Above described components are related to Browser-provided metadata vocabulary. The lower component is related to custom metadata. Click button  to launch the function:


Just fill up the blanks as instructed in the example:


Press button  to make the new metadata term:


And check the checkbox following "my friends" to display the term in metadata color map:


The custom metadata terms can be saved in session function.



2. Annotating custom bigWig tracks

At control panel, go to "Tracks" > "Custom track", and click tab "bigWig" to show the custom bigWig track submission panel:


When submitting a custom bigwig track, you can make metadata annotation to it, and this step is optional. You can always add or edit metadata annotation at a later stage.

Click button , the metadata management panel appears:


Open up the vocabulary tree and find terms to annotate the custom track. Only leaf-level terms can be used by checking the checkboxes, the term will be displayed in a new table:


You can select an attribute from the custom term we created above to have it displayed in this table:


Notice the difference of how server-provided and custom terms are presented in the table. Click X to remove term from the table.

Click button  to submit the track. Here we give it a dummy name "aa bb". Right click on the track in genome heatmap and option "Edit metadata" can be seen in the menu:


Select the option to open the metadata editing panel in floating toolbox, the existing metadata of this track will be shown here:


You can repeat the same procedures to add or remove metadata entries for this track. The metadata color map will update on the fly.